Align Basic amino acid uptake transporter, BgtAB (characterized)
to candidate WP_083767305.1 MVAN_RS31485 ABC transporter substrate-binding protein
Query= TCDB::Q8YSA2 (501 letters) >NCBI__GCF_000015305.1:WP_083767305.1 Length = 487 Score = 258 bits (660), Expect = 3e-73 Identities = 171/482 (35%), Positives = 251/482 (52%), Gaps = 22/482 (4%) Query: 12 VLSLICLFLTGC----SGN-LSQGKTLRIATEPAFPPFEFTAQG-GNLQGFSIDLMNAIA 65 VL+ I + LT C SGN + LR+ TE + PF + G L G+ +D+ A+ Sbjct: 11 VLAAIAVLLTACGSSGSGNPVESSGVLRVGTEGVYAPFSYHDPATGQLTGYDVDVARAVG 70 Query: 66 SAANLKVNFQSLPFDGIIPALQSRTVDAAISSITITAERAETVAFSRPYFKAGLAIAIRS 125 + V F P+D I AL++ D + +TIT ER + S PY I R+ Sbjct: 71 EKLGVNVEFVETPWDSIFAALEANRFDVVANQVTITPERQQKYDLSEPYSIGEGVIVTRA 130 Query: 126 SNEDITGFDSLKNKKIAVQIGTTGAGKAKSIPGAQIRSFDSAPLALQELLNNNVDAVIND 185 ++ IT L+ K+ A + AG A+ GAQI S + A+ L VD V+ND Sbjct: 131 DDDSITSLADLRGKRAAQSTTSNWAGVARDA-GAQIESVEGLTQAMALLSQGRVDVVVND 189 Query: 186 APVTLYA-INTGNLQGIKVVEKLLTEEYYGIATAQNSPYLALINDGLNRVLADGSYSQIY 244 + +++YA + N +K+ + G A +NS L +N L + ADG+ ++I Sbjct: 190 S-LSIYAYLAETNDTAVKIAGATGEKSEQGFAARKNSGLLPDLNTALEELKADGTLAEIS 248 Query: 245 QKWFKVEPPSLPDKSLYENQTNTHKSGSINLILQFLPTLLQGAL-VTIQLTILSTVLGLI 303 QK+ K + S ++ T ++ L+L L L + AL +TI LTI+S V+GL+ Sbjct: 249 QKYLKT------NASGGQDAPQTQPRSALRLVLDNLWPLARAALTMTIPLTIISFVIGLV 302 Query: 304 CGTLIALTRLSQFTPARLFARAYVDFFRGTPLLVQIFMIYFGIPALAQQLGFTFNFDRWV 363 +AL RLS AR Y+ RGTPLLVQ+F+++F +P F D + Sbjct: 303 IALGVALARLSSNVVLTNLARFYISVIRGTPLLVQLFIVFFALPE------FGVRIDPFP 356 Query: 364 AGVIALSVNAAAYIAEIVRAGIQSIETGQTEAAKSLGLNPWLTMRLVIFPQAFRRMLPPL 423 A VIA S+N Y AEI+R+ IQSI GQ EAA+++GLN T+R +I PQA R +PPL Sbjct: 357 AAVIAFSLNVGGYAAEIIRSAIQSIPKGQWEAAETIGLNYAGTLRRIILPQATRVAVPPL 416 Query: 424 GNEFISLLKDTSLVAVIGFEELFRKGQLIVADNYRAFEIYAAVAIVYLCLTLLASQVLSR 483 N ISL+KDTSL + I EL R+ Q+I A + F +Y A+ Y + L+ S +R Sbjct: 417 SNTLISLVKDTSLASTILVTELLRQAQIIAAPTFEFFALYGTAAVYYWVICLVLSFGQAR 476 Query: 484 LE 485 E Sbjct: 477 FE 478 Lambda K H 0.323 0.137 0.394 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 503 Number of extensions: 22 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 501 Length of database: 487 Length adjustment: 34 Effective length of query: 467 Effective length of database: 453 Effective search space: 211551 Effective search space used: 211551 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (22.0 bits) S2: 52 (24.6 bits)
This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory